OEDesignUnit¶
Attention
This API is currently available in C++ and Python.
class OEDesignUnit : public OESystem::OEBase
This is a container class derived from OEBase that holds all molecules needed to construct a model-ready biomolecular system.
Molecule constructors¶
Note
Molecule constructors are intended for already prepared molecules. They requires a target structure, as well as either a ligand or a list of binding site residues. Solvent and co-factors are optional, and are only set if the molecules passed are valid. The target molecule is not split into components and no structure preparation take place. A title will be generated based on the names of the provided molecules, but can be set manually afterwards.
OEDesignUnit(const OEChem::OEMolBase& target, const OEChem::OEMolBase& ligand, const OEChem::OEMolBase& solvent=OEChem::OEGraphMol(), const OEChem::OEMolBase& cofactors=OEChem::OEGraphMol(), const unsigned targetID=OEDesignUnitComponents::Protein)
Target-ligand constructor
OEDesignUnit(const OEChem::OEMolBase& target, const std::vector<std::string>& siteResidues, const OEChem::OEMolBase& solvent=OEChem::OEGraphMol(), const OEChem::OEMolBase& cofactors=OEChem::OEGraphMol(), const unsigned targetID=OEDesignUnitComponents::Protein);
Apo target constructor
operator=¶
operator bool¶
Clear¶
CreateCopy¶
CreateCopy(OEDesignUnit self)
Deep copy constructor that returns a copy of the object. The memory for the returned OEDesignUnit object is dynamically allocated and owned by the caller.
GetComponent¶
GetComponent(OEDesignUnit self, OEMolBase molecule, componentID)
Returns a const reference to the molecule on the OEDesignUnit that is associated with the input componentID.
GetComponentID¶
GetComponentID(OEDesignUnit self, componentTag)
Returns the internal unsigned integer representation of the componentTag string from the OEDesignUnit object.
GetComponentTag¶
GetComponentTag(OEDesignUnit self, componentID)
Returns the string tag representation of the componentID unsigned integer from the OEDesignUnit object.
GetComponents¶
GetComponents(self, *args)
GetComponents(OEDesignUnit self, OEMolBase mol, unsigned int componentMask, bool bondCovalent=True)
GetComponents(OEDesignUnit self, OEMolBase mol, unsigned int componentMask)
GetComponents(OEDesignUnit self, OEMolBase mol)
The function creates a single output mol from the components
given in the componentMask bit mask. The bit mask can be
constructed using unsigned integers stored in the
OEDesignUnitComponents namespace. The
function returns a boolean value to alert if the operation was
successful. Note that this function only works for a list of components (e.g. other_ligands, excipients, etc).
The optional predicate can be used to subset some of the components
in the specified bit mask. The predicate does not have to be complete,
e.g. two water molecules can be specified to subset the solvent category,
but that will not subset the protein component also included in that mask.
In essence the predicate is checked to see if it matches part of a design unit
component and only in this case does it take effect.
GetComponentsWithin¶
GetComponentsWithin(self, *args)
GetComponentsWithin(OEDesignUnit self, OEMolBase mol, unsigned int componentMask, unsigned int withinMask, double dist=5.0, bool includeSelf=False, bool bondCovalent=True)
GetComponentsWithin(OEDesignUnit self, OEMolBase mol, unsigned int componentMask, unsigned int withinMask, double dist=5.0, bool includeSelf=False)
GetComponentsWithin(OEDesignUnit self, OEMolBase mol, unsigned int componentMask, unsigned int withinMask, double dist=5.0)
GetComponentsWithin(OEDesignUnit self, OEMolBase mol, unsigned int componentMask, unsigned int withinMask)
GetComponentsWithin(OEDesignUnit self, OEMolBase mol, unsigned int componentMask)
GetComponentsWithin(OEDesignUnit self, OEMolBase mol)
The function creates a single output mol from the components
given in the componentMask bit mask that fall within a dist
distance of components given in the withinMask bit mask. All bit
masks can be constructed using unsigned integers stored in the
OEDesignUnitComponents namespace. If the
boolean bondCovalent flag is set, all components that should be
covalently bonded will have bonded added in the output mol. The
function returns a boolean value to alert if the operation was
successful.
GetDataType¶
GetDataType(OEDesignUnit self)
This pure virtual function is used to perform run-time type
identification. The value returned by the method should be
equivalent to the value returned by OEGetDataType
using the OEDesignUnit derived class type as the template argument.
GetIDs¶
GetIDs(OEDesignUnit self)
Returns a vector of the component IDs stored on the OEDesignUnit object.
GetLigand¶
GetLigand(OEDesignUnit self, OEMolBase molecule)
Returns success based on a valid copy of the ligand molecule in the OEDesignUnit object.
lig = oechem.OEGraphMol()
if not du.GetLigand(lig):
oechem.OEThrow.Fatal("Error: Could not extract ligand from the OEDesignUnit.")
oechem.OEWriteMolecule(ofs, lig)
Whole example script can be downloaded from here.
GetMetal¶
GetMetal(OEDesignUnit self, OEMolBase molecule)
Returns success based on a valid copy of the metal in the OEDesignUnit object.
GetNucleicAcid¶
GetNucleicAcid(OEDesignUnit self, OEMolBase molecule)
Returns success based on a valid copy of the nucleic acid molecule in the OEDesignUnit object.
GetPDBMetaData¶
GetPDBMetaData(OEDesignUnit self, OEMolBase mol)
Returns success based on a valid copy of the PDB metadata in the OEDesignUnit object.
See also
OEResidueToString function.
GetPackingResidues¶
GetPackingResidues(OEDesignUnit self, OEMolBase molecule)
Returns success based on a valid copy of the packing residue molecule in the OEDesignUnit object.
GetProtein¶
GetProtein(OEDesignUnit self, OEMolBase molecule)
Returns success based on a valid copy of the protein molecule in the OEDesignUnit object.
GetReceptor¶
GetReceptor(self, *args)
GetReceptor(OEDesignUnit self, OEReceptor receptor)
Returns a reference to the receptor on the OEDesignUnit object.
GetReceptor(OEDesignUnit self)
Returns success based on a valid copy of the receptor in the OEDesignUnit object.
GetSiteResidues¶
GetSiteResidues(OEDesignUnit self)
Returns a vector of the site residue strings stored on the OEDesignUnit object. This function calls the OEResidueToString function with “:” delimiter.
GetSolvent¶
GetSolvent(OEDesignUnit self, OEMolBase molecule)
Returns success based on a valid copy of the solvent molecule in the OEDesignUnit object.
GetStructureQuality¶
GetStructureQuality(OEDesignUnit self)
Returns the OEStructureQuality class stored on the OEDesignUnit object.
See also
OEStructureQuality class
GetTransform¶
GetTransform(OEDesignUnit self, OETrans trans)
Returns success based on a valid copy of the input OETrans object in the OEDesignUnit object.
See also
OETrans class
GetTaggedComponents¶
GetTaggedComponents(self, *args)
GetTaggedComponents(OEDesignUnit self, unsigned int componentMask)
GetTaggedComponents(OEDesignUnit self)
Returns an OEIter of all molecules and
corresponding molecular tags stored on the OEDesignUnit
object. A bit mask of desired components can be constructed from
constants in the OEDesignUnitComponents
namespace and be passed in via the componentMask argument.
GetTags¶
GetTags(OEDesignUnit self)
Returns a vector of the tags of the molecules stored on the OEDesignUnit object.
GetTarget¶
GetTarget(OEDesignUnit self, OEMolBase molecule)
Returns success based on a valid copy of the target molecule in the OEDesignUnit object.
GetTargetComponentID¶
GetTargetComponentID(OEDesignUnit self)
Returns the component ID from the
OEDesignUnitComponents namespace of the
target molecule on the OEDesignUnit object.
GetTargetComponentTag¶
GetTargetComponentTag(OEDesignUnit self)
Returns the string tag of the title of the OEDesignUnit object.
HasAltLoc¶
HasComponent¶
HasComponent(OEDesignUnit self, unsigned int componentID)
Checks that a molecule given by the componentID from the
OEDesignUnitComponents namespace has been
set on the OEDesignUnit object.
HasLigand¶
HasLigand(OEDesignUnit self)
Checks that the ligand molecule of the OEDesignUnit object has been set.
HasMetal¶
HasMetal(OEDesignUnit self)
Checks that the metal molecule of the OEDesignUnit object has been set.
HasNucleicAcid¶
HasNucleicAcid(OEDesignUnit self)
Checks that the nucleic acid molecule of the OEDesignUnit object has been set.
HasPDBMetaData¶
HasPDBMetaData(OEDesignUnit self)
Checks that the PDB metadata of the OEDesignUnit object has been set.
HasPackingResidues¶
HasPackingResidues(OEDesignUnit self)
Checks that the packing residue molecule of the OEDesignUnit object has been set.
HasProtein¶
HasProtein(OEDesignUnit self)
Checks that the protein molecule of the OEDesignUnit object has been set.
HasReceptor¶
HasReceptor(OEDesignUnit self)
Checks that the OEDesignUnit object contains a valid receptor.
HasSiteResidues¶
HasSiteResidues(OEDesignUnit self)
Checks that the site residues of the OEDesignUnit object has been set.
HasSolvent¶
HasSolvent(OEDesignUnit self)
Checks that the solvent molecule of the OEDesignUnit object has been set.
HasStructureQuality¶
HasStructureQuality(OEDesignUnit self)
Checks that the internal OEStructureQuality object stored on the OEDesignUnit has been set.
HasTransform¶
HasTransform(OEDesignUnit self)
Checks that the internal OETrans object stored on the OEDesignUnit has been set.
HasTarget¶
HasTitle¶
IsDataType¶
IsDataType(OEDesignUnit self, void const * arg2)
Returns whether the type is the same as the instance this method is called on.
ClearComponent¶
bool ClearComponent(OEDesignUnit self, const std::string& componentTag, int listIndex = -1) bool ClearComponent(OEDesignUnit self, unsigned componentID, int listIndex = -1)Clears a specified component. The listIndex is intended for listComponents, e.g. co-factors. If the listIndex is -1 the entire list is removed, otherwise only the co-factor with the given index is removed.